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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Expansion of Carbon Calculator for Land Use and Land Management Change from Biofuels Production (CCLUB) to Address Induced Land Use Changes and Other Indirect Effects of Clean Fuel Production for R&D GREET ® 2024

Since the late 2000s, biofuel life-cycle analysis (LCA) has included induced land use change (ILUC) and other indirect effects (I-effects) of large-scale feedstock production for biofuels. In ILUC and I-effect emissions modeling, economic models are used to simulate the area of land conversion among different land types and other I-effects such as non-feedstock crop production and livestock production that are driven by the scenarios of biofuel production volume shocks. On the other hand, emission factors (EF) models estimate carbon stock changes and GHG emissions associated with these changes. Finally, the area and type of ILUC and I-effects are combined with the EFs to estimate the biofuel ILUC/I-effect GHG emissions in the unit of grams of CO 2 equivalent per MJ biofuel produced (g CO 2 e/MJ).

09 BIOMASS FUELS↗
DOE OSTI2025

​​Updates to Anaerobic Digestion Pathways for Animal Manure in R&D GREET 2025​

Livestock and poultry manure management in the U.S. is a greenhouse gas (GHG) intensive process, emitting 81.7 MMT CO 2 e in 2022 (1.5% of net U.S. GHG emissions). The primary GHG is methane (CH 4 ), with 2,312 kt released in 2022 (9% of U.S. CH 4 emissions). Manure management methods are commonly categorized by whether they are anaerobic (“wet”) or aerobic (“dry”) techniques. Although dry methods manage the largest share of manure, the majority of GHG emissions are generated during storage of manure in anaerobic conditions – typically in water-filled tanks, pits, or lagoons. There has been a 65% increase in emissions from 1990, primarily due to an increasing cattle population. Also, this rise in population has been coupled with a rise in animal confinement and density, which typically adopt wet manure management methods. Within wet methods, anaerobic bacteria proliferate and decompose volatile solids (VS) within the manure in a process called anaerobic digestion to produce roughly equal mixtures of CH 4 and carbon dioxide (CO 2 ). These GHGs are fugitive, in that they are assumed to be released to the atmosphere and contribute to GHGs within U.S. GHG inventories. If the methane is captured and purified (i.e., “upgraded”) this simultaneously mitigates GHGs that would have otherwise been released and produces a valuable energy product known colloquially as Renewable Natural Gas (RNG). Such processes are acknowledged by U.S. policy through programs such as the U.S. Renewable Fuels Standard (RFS), the federal Clean Fuel Production Credit (45Z), and state clean fuel standards (CFS). In the 45Z and CFS schemes, the GHG emissions of the business-as-usual (BAU) manure management system is taken as a baseline, and credits are received based on GHG reductions relative to this baseline. Thus, estimating the GHG emissions of the BAU scenario (also known as the “counterfactual”) is necessary.

09 BIOMASS FUELS↗
DOE OSTI2024

Building a FAIR data ecosystem for incorporating single-cell transcriptomics data into agricultural genome to phenome research

Introduction The agriculture genomics community has numerous data submission standards available, but the standards for describing and storing single-cell (SC, e.g., scRNA- seq) data are comparatively underdeveloped. Methods To bridge this gap, we leveraged recent advancements in human genomics infrastructure, such as the integration of the Human Cell Atlas Data Portal with Terra, a secure, scalable, open-source platform for biomedical researchers to access data, run analysis tools, and collaborate. In parallel, the Single Cell Expression Atlas at EMBL-EBI offers a comprehensive data ingestion portal for high-throughput sequencing datasets, including plants, protists, and animals (including humans). Developing data tools connecting these resources would offer significant advantages to the agricultural genomics community. The FAANG data portal at EMBL-EBI emphasizes delivering rich metadata and highly accurate and reliable annotation of farmed animals but is not computationally linked to either of these resources. Results Herein, we describe a pilot-scale project that determines whether the current FAANG metadata standards for livestock can be used to ingest scRNA-seq datasets into Terra in a manner consistent with HCA Data Portal standards. Importantly, rich scRNA-seq metadata can now be brokered through the FAANG data portal using a semi-automated process, thereby avoiding the need for substantial expert curation. We have further extended the functionality of this tool so that validated and ingested SC files within the HCA Data Portal are transferred to Terra for further analysis. In addition, we verified data ingestion into Terra, hosted on Azure, and demonstrated the use of a workflow to analyze the first ingested porcine scRNA-seq dataset. Additionally, we have also developed prototype tools to visualize the output of scRNA-seq analyses on genome browsers to compare gene expression patterns across tissues and cell populations. This JBrowse tool now features distinct tracks, showcasing PBMC scRNA-seq alongside two bulk RNA-seq experiments. Discussion We intend to further build upon these existing tools to construct a scientist-friendly data resource and analytical ecosystem based on Findable, Accessible, Interoperable, and Reusable (FAIR) SC principles to facilitate SC-level genomic analysis through data ingestion, storage, retrieval, re-use, visualization, and comparative annotation across agricultural species.

Genetics & Heredity↗
DOE OSTI2022

Establishment of a reverse transcription real-time quantitative PCR method for Getah virus detection and its application for epidemiological investigation in Shandong, China

Getah virus (GETV) is a mosquito-borne, single-stranded, positive-sense RNA virus belonging to the genus Alphavirus of the family Togaviridae . Natural infections of GETV have been identified in a variety of vertebrate species, with pathogenicity mainly in swine, horses, bovines, and foxes. The increasing spectrum of infection and the characteristic causing abortions in pregnant animals pose a serious threat to public health and the livestock economy. Therefore, there is an urgent need to establish a method that can be used for epidemiological investigation in multiple animals. In this study, a real-time reverse transcription fluorescent quantitative PCR (RT-qPCR) method combined with plaque assay was established for GETV with specific primers designed for the highly conserved region of GETV Nsp1 gene. The results showed that after optimizing the condition of RT-qPCR reaction, the minimum detection limit of the assay established in this study was 7.73 PFU/mL, and there was a good linear relationship between viral load and Cq value with a correlation coefficient ( R 2 ) of 0.998. Moreover, the method has good specificity, sensitivity, and repeatability. The established RT-qPCR is 100-fold more sensitive than the conventional RT-PCR. The best cutoff value for the method was determined to be 37.59 by receiver operating characteristic (ROC) curve analysis. The area under the curve (AUC) was 0.956. Meanwhile, we collected 2,847 serum specimens from swine, horses, bovines, sheep, and 17,080 mosquito specimens in Shandong Province in 2022. The positive detection rates by RT-qPCR were 1%, 1%, 0.2%, 0%, and 3%, respectively. In conclusion, the method was used for epidemiological investigation, which has extensive application prospects.

Cao, Xinyu↗
DOE OSTI2022

Dissemination of blaNDM-5 and mcr-8.1 in carbapenem-resistant Klebsiella pneumoniae and Klebsiella quasipneumoniae in an animal breeding area in Eastern China

Animal farms have become one of the most important reservoirs of carbapenem-resistant Klebsiella spp. (CRK) owing to the wide usage of veterinary antibiotics. “One Health”-studies observing animals, the environment, and humans are necessary to understand the dissemination of CRK in animal breeding areas. Based on the concept of “One-Health,” 263 samples of animal feces, wastewater, well water, and human feces from 60 livestock and poultry farms in Shandong province, China were screened for CRK. Five carbapenem-resistant Klebsiella pneumoniae (CRKP) and three carbapenem-resistant Klebsiella quasipneumoniae (CRKQ) strains were isolated from animal feces, human feces, and well water. The eight strains were characterized by antimicrobial susceptibility testing, plasmid conjugation assays, whole-genome sequencing, and bioinformatics analysis. All strains carried the carbapenemase-encoding gene bla NDM-5 , which was flanked by the same core genetic structure (IS 5 - bla NDM-5 - ble MBL - trpF - dsbD -IS 26 -IS Kox3 ) and was located on highly related conjugative IncX3 plasmids. The colistin resistance gene mcr-8.1 was carried by three CRKP and located on self-transmissible IncFII(K)/IncFIA(HI1) and IncFII(pKP91)/IncFIA(HI1) plasmids. The genetic context of mcr-8.1 consisted of IS 903 - orf - mcr-8.1-copR-baeS-dgkA - orf -IS 903 in three strains. Single nucleotide polymorphism (SNP) analysis confirmed the clonal spread of CRKP carrying- bla NDM-5 and mcr-8.1 between two human workers in the same chicken farm. Additionally, the SNP analysis showed clonal expansion of CRKP and CRKQ strains from well water in different farms, and the clonal CRKP was clonally related to isolates from animal farms and a wastewater treatment plant collected in other studies in the same province. These findings suggest that CRKP and CRKQ are capable of disseminating via horizontal gene transfer and clonal expansion and may pose a significant threat to public health unless preventative measures are taken.

Yang, Chengxia↗
DOE OSTI2020

Extinction Dynamics of the Foot-and-Mouth Disease Virus Carrier State Under Natural Conditions

Foot-and-mouth disease (FMD) is one of the most economically important livestock diseases worldwide. Following the clinical phase of FMD, a large proportion of ruminants remain persistently infected for extended periods. Although extinction of this carrier state occurs continuously at the animal and population levels, studies vary widely in their estimates of the duration of persistent infection. There is a need for robust statistical models to capture the dynamics of persistent infection for the sake of guiding FMD control and trade policies. The goal of the current study was to develop and assess statistical models to describe the extinction of FMD virus (FMDV) persistent infection using data from primary longitudinal studies of naturally infected cattle and Asian buffalo in Vietnam and India. Specifically, accelerated failure time (AFT) models and generalized linear mixed models (GLMM) were developed to predict the probability of persistent infection in seropositive animals and identified carriers at the individual animal level at sequential time points after outbreaks. The primary studies were analyzed by country and combined using an individual-participant data meta-analysis approach. The models estimated similar trends in the duration of persistent infection for the study/species groups included in the analyses, however the significance of the trends differed between the models. The overall probabilities of persistent infection were similar as predicted by the AFT and GLMM models: 6 months: 99% (AFT) /80% (GLMM), 12 months: 51% (AFT) /32% (GLMM), 18 months: 6% (AFT) /5% (GLMM), 24 months: 0.8% (AFT) /0.6% (GLMM). These models utilizing diverse and robust data sets predict higher probabilities of persistence than previously published, suggesting greater endurance of carriers subsequent to an outbreak. This study demonstrates the utility of statistical models to investigate the dynamics of persistent infection and the importance of large datasets, which can be achieved by combining data from several smaller studies in meta-analyses. Results of this study enhance current knowledge of the FMDV carrier state and may inform policy decisions regarding FMDV persistent infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Epidemiologic and economic considerations regarding persistently infected cattle during vaccinate-to-live strategies for control of foot-and-mouth disease in FMD-free regions

Development of a foot-and-mouth disease (FMD) carrier state following FMD virus (FMDV) infection is a well-established phenomenon in cattle. However, the proportion of cattle likely to become carriers and the duration of the carrier state at a herd or population-level are incompletely understood. The objective of this study was to examine the epidemiologic and economic impacts of vaccination-to-live strategy in a disease-free region or country. We developed and simulated scenarios of FMD spread and control in the US livestock population, which included depopulation for a limited period, followed by a vaccinate-to-live strategy with strong biosecurity and movement restrictions. Six scenarios of FMD spread and control were simulated in the InterSpread Plus (ISP) modeling tool. Data on the number of infected and depopulated cattle (by operation types) from ISP model runs were used to estimate the monthly number of infected but not depopulated (potential carrier) cattle after the infection. Using available literature data on the FMD carrier state, we estimated the monthly proportion of carrier cattle (from infected but not depopulated cattle) over time following infection. Among the simulated scenarios, the median (25th, 75th percentile) number of infected cattle ranged from 43,217 (42,819, 55,274) head to 148,907 (75,819, 205,350) head, and the epidemic duration ranged from 20 (11, 30) to 76 (38, 136) days. In general, larger outbreaks occurred when depopulation was carried out through longer periods, and the onset of the vaccination was late (p > 0.05). The estimated proportion of surviving cattle, which were infected and not depopulated and had the potential to become persistently infected ranged from 14 to 35% of total infected cattle. Production losses in beef and dairy sectors were higher when outbreaks started in multiple states simultaneously, but production losses were small compared to trade losses and consumer avoidance losses. These results can be used to inform the consideration of a vaccinate-to-live strategy for FMD outbreaks and the development of appropriate post-outbreak management strategies. Furthermore, this output will enable a more detailed examination of the epidemiologic and economic implications of allowing convalescent cattle to survive and remain in production chains after FMD outbreaks in FMD-free regions.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Assessment of a reconfiguration of the InterSpread Plus US national FMD model as a potential tool to analyze a foot-and-mouth disease outbreak on a single large cattle feedlot in the United States

An incursion of foot-and-mouth disease (FMD) into the United States remains a concern of high importance and would have devastating socioeconomic impacts to the livestock and associated industries. This highly transmissible and infectious disease poses continual risk for introduction into the United States (US), due to the legal and illegal global movement of people, animals, and animal products. While stamping out has been shown to effectively control FMD, depopulation of large cattle feedlots (>50,000 head) presents a number of challenges for responders due to the resources required to depopulate and dispose of large numbers of animals in a timely and effective manner. However, evaluating alternative strategies for FMD control on large feedlots requires a detailed within-farm modeling approach, which can account for the unique structure of these operations. To address this, we developed a single feedlot, within-farm spread model using a novel configuration within the InterSpread Plus (ISP) framework. As proof of concept we designed six scenarios: (i) depopulation - the complete depopulation of the feedlot, (ii) burn-through – a managed “burn-through” where the virus is allowed to spread through the feedlot and only movement restriction and biosecurity are implemented, (iii) firebreak-NV – targeted depopulation of infected pens and adjacent pens without vaccination; (iv) firebreak - targeted depopulation of infected pens and adjacent pens with vaccination of remaining pens; (v) harvest-NV - selective harvest of pens where a 100% movement restriction is applied for 28-30 days, then pens are set for selection to be sent to slaughter, while allowing a controlled “burn-through” without vaccination; and (vi) harvest - selective harvest of pens with vaccination. Overall, the burn-through scenario (ii) had the shortest epidemic duration (31d (30, 33)) median (25th, 75th percentiles), while the firebreak scenario (iv) had the longest (47d (38,55)). Additionally, we found that scenarios implementing depopulation delayed the peak day of infection and reduced the total number of pens infected compared to non-depopulation scenarios.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Mitigation of Gaseous Emissions from Stored Swine Manure with Biochar: Effect of Dose and Reapplication on a Pilot-Scale

Rural communities are affected by gaseous emissions from intensive livestock production. Practical mitigation technologies are needed to minimize emissions from stored manure and improve air quality inside barns. In our previous research, the one-time surficial application of biochar to swine manure significantly reduced emissions of NH3 and phenol. We observed that the mitigation effect decreased with time during the 30-day trials. In this research, we hypothesized that bi-weekly reapplication of biochar could improve the mitigation effect on a wider range of odorous compounds using a larger scale and longer trials. The objective was to evaluate the effectiveness of biochar dose and reapplication on mitigation of targeted gases (NH3, odorous, volatile organic compounds VOCs, odor, greenhouse gases (GHG)) from stored swine manure on a pilot-scale setup over 8-weeks. The bi-weekly reapplication of the lower biochar dose (2 kg/m2) showed much higher significant percentage reductions in emissions for NH3 (33% without and 53% with reapplication) and skatole (42% without and 80% with reapplication), respectively. In addition, the reapplication resulted in the emergence of a statistical significance to the mitigation effect for all other targeted VOCs. Specifically, for indole, the percentage reduction improved from 38% (p = 0.47, without reapplication) to 78% (p = 0.018, with reapplication). For phenol, the percentage reduction improved from 28% (p = 0.71, without reapplication) to 89% (p = 0.005, with reapplication). For p-cresol, the percentage reduction improved from 31% (p = 0.86, without reapplication) to 74% (p = 0.028, with reapplication). For 4-ethyl phenol, the percentage emissions reduction improved from 66% (p = 0.44, without reapplication) to 87% (p = 0.007, with reapplication). The one-time 2 kg/m2 and 4 kg/m2 treatments showed similar effectiveness in mitigating all targeted gases, and no statistical difference was found between the dosages. The one-time treatments showed significant percentage reductions of 33% and 42% and 25% and 48% for NH3 and skatole, respectively. The practical significance is that the higher (one-time) biochar dose may not necessarily result in improved performance over the 8-week manure storage, but the bi-weekly reapplication showed significant improvement in mitigating NH3 and odorous VOCs. The lower dosages and the frequency of reapplication on the larger-scale should be explored to optimize biochar treatment and bring it closer to on-farm trials.

Chen, Baitong (ORCID:0000000266071253)↗
DOE OSTI2021

Mitigation of Acute Hydrogen Sulfide and Ammonia Emissions from Swine Manure during Three-Hour Agitation Using Pelletized Biochar

The risk of inhalation exposure to elevated concentrations of hydrogen sulfide (H2S) and ammonia (NH3) during the agitation of stored swine manure is high. Once or twice a year, farmers agitate manure before pump-out and application to fields. Agitation of the swine manure causes the short-term releases of highly toxic levels of H2S and NH3. In our previous pilot-scale studies, the biochar powder showed significant mitigation of H2S and NH3 emissions when it was surficially applied to manure immediately before agitation. However, fine biochar powder application poses hazards by itself and may not be practical to apply on a farm scale, especially when livestock and workers are present. We hypothesized that applying pelletized biochar to manure surfaces is just as effective as applying powder to protect farmers and animals from excessive exposure to H2S and NH3. This work reports on the lab-scale proof-of-the-concept trials with biochar pellets on the lab scale. The objective was to compare the biochar pellets and biochar powder on their effectiveness of mitigation on H2S and NH3 gases during 3-h-long swine manure agitation. Three scenarios were compared in (n = 3) trials: (i) control, (ii) 12.5 mm thick surficial application to manure surface of biochar powder, and (iii) an equivalent (by mass) dose of pelletized biochar applied to the manure surface. The biochar powder was bound with 35% (wt) water into ~5 × 10 mm (dia × length) pellets. The biochar powder was significantly (p < 0.05) more effective than the biochar pellets. Still, pellets reduced total H2S and NH3 emissions by ~72% and ~68%, respectively (p = 0.001), compared with ~99% by powder (p = 0.001). The maximum H2S and NH3 concentrations were reduced from 48.1 ± 4.8 ppm and 1810 ± 850 ppm to 20.8 ± 2.95 ppm and 775 ± 182 ppm by pellets, and to 22.1 ± 16.9 ppm and 40.3 ± 57 ppm by powder, respectively. These reductions are equivalent to reducing the maximum concentrations of H2S and NH3 during the 3-h manure agitation by 57% and 57% (pellets) and 54% and 98% (powder), respectively. Treated manure properties hinted at improved nitrogen retention, yet they were not significant due to high variability. We recommend scaling up and trials on the farm-scale level using biochar pellets to assess the feasibility of application to large manure surfaces and techno-economic evaluation.

Chen, Baitong (ORCID:0000000266071253)↗
DOE OSTI2023

Near-Term Effects of Perennial Grasses on Soil Carbon and Nitrogen in Eastern Nebraska

Incorporating native perennial grasses adjacent to annual row crop systems managed on marginal lands can increase system resiliency by diversifying food and energy production. This study evaluated (1) soil organic C (SOC) and total N stocks (TN) under warm-season grass (WSG) monocultures and a low diversity mixture compared to an adjacent no-till continuous-corn system, and (2) WSG total above-ground biomass (AGB) in response to two levels of N fertilization from 2012 to 2017 in eastern Nebraska, USA. The WSG treatments consisted of (1) switchgrass (SWG), (2) big bluestem (BGB), and (3) low-diversity grass mixture (LDM; big bluestem, Indiangrass, and sideoat grama). Soils were sampled at fixed depth increments (0–120 cm) in the WSG plots and in the adjacent corn experiment in 2012 and 2017. Soil stocks (Mg ha−1) of SOC and TN were calculated on an equivalent soil mass (ESM) basis and compared within the three WSG treatments as well as between experiments (corn compared to the mean of all WSGs). Soil organic C and TN stocks within soil layers and cumulative stocks responded to the main effect of WSG (PWSG < 0.05) but were no different when comparing the WSGs to corn (Pexpt = NS). Both SOC/TN stocks and cumulative stocks were generally greater in the LDM compared to the BGB. Neither SOC nor TN changed over time under either the WSGs or corn. Warm-season grass AGB responded to a three-way interaction of year, N rate, and WSG (p = 0.0007). Decreases in AGB over time were significant across WSGs and N levels except for SWG at 56 kg N ha−1 and LDM at 112 kg N ha−1. Above-ground biomass was generally greater in the LDM after the first harvest year (2013). Results suggest that incorporating WSGs into marginal cropland can maintain SOC and TN stocks while providing a significant source of biomass to be used in energy production or in integrated livestock systems.

Ramirez, II, Salvador (ORCID:000000030152153X)↗
DOE OSTI2021

Molecular Pathogenesis and Immune Evasion of Vesicular Stomatitis New Jersey Virus Inferred from Genes Expression Changes in Infected Porcine Macrophages

The molecular mechanisms associated with the pathogenesis of vesicular stomatitis virus (VSV) in livestock remain poorly understood. Several studies have highlighted the relevant role of macrophages in controlling the systemic dissemination of VSV during infection in different animal models, including mice, cattle, and pigs. To gain more insight into the molecular mechanisms used by VSV to impair the immune response in macrophages, we used microarrays to determine the transcriptomic changes produced by VSV infection in primary cultures of porcine macrophages. The results indicated that VSV infection induced the massive expression of multiple anorexic, pyrogenic, proinflammatory, and immunosuppressive genes. Overall, the interferon (IFN) response appeared to be suppressed, leading to the absence of stimulation of interferon-stimulated genes (ISG). Interestingly, VSV infection promoted the expression of several genes known to downregulate the expression of IFNβ. This represents an alternate mechanism for VSV control of the IFN response, beyond the recognized mechanisms mediated by the matrix protein. Although there was no significant differential gene expression in macrophages infected with a highly virulent epidemic strain compared to a less virulent endemic strain, the endemic strain consistently induced higher expression of all upregulated cytokines and chemokines. Collectively, this study provides novel insights into VSV molecular pathogenesis and immune evasion that warrant further investigation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Tropical Red Macroalgae Cultivation with a Focus on Compositional Analysis

To create carbon efficient sources of bioenergy feedstocks and feedstuff for aquaculture and terrestrial livestock, it is critical to develop and commercialize the most efficient seaweed cultivation approach with a sustainable nutrient input supply. Here, we present data for a novel, onshore tropical macroalgae cultivation system, based on influent deep seawater as the nutrient and carbon sources. Two red algal species were selected, Agardhiella subulata and Halymenia hawaiiana, as the basis for growth optimization. Highest productivity in small-scale cultivation was demonstrated with A. subulata in the 10% deep seawater (64.7 µg N L−1) treatment, growing at up to 26% specific growth rate day−1 with highest yields observed at 247.5 g m−2 day−1 fresh weight. The highest yields for H. hawaiiana were measured with the addition of 10% deep seawater up to 8.8% specific growth rate day−1 and yields at 63.3 g fresh weight m−2 day−1 equivalent. Biomass should be culled weekly or biweekly to avoid density limitations, which likely contributed to a decrease in SGR over time. With a measured 30–40% carbon content of the ash-free dry weight (20–30% of the dry weight) biomass, this translates to an almost 1:1 CO2 capture to biomass ratio. The compositional fingerprint of the high carbohydrate content of both Agardhiella and Halymenia makes for an attractive feedstock for downstream biorefinery applications. By focusing on scaling and optimizing seaweed farming technologies for large-scale onshore farms, the opportunities for yield potential, adaptability to cultivation conditions, and meeting global sustainability goals through novel, carbon-negative biomass sources such as seaweed can be realized.

09 BIOMASS FUELS↗
DOE OSTI2020

Soil Carbon Change Due to Land Conversion to Grassland in a Semi-Arid Environment

A 5-year study evaluated the change in the quantity of soil total C (STC), soil organic C (SOC), and soil inorganic C (SIC) stored in the surface 60 cm of the soil profile on two adjacent blocks of land with a long-term history of cropping (CH) or undisturbed grassland (NH) on similar soil types between 1999 and 2004. The NH area was tilled and a grass-legume species mix was seeded into plots on both the NH and the CH areas. Selected plots of restored grass were established so they could be grazed (GG) by livestock while other plots were left ungrazed (UG). Original undisturbed (and ungrazed) grassland plots within the NH area were used as a control treatment. Initially, STC and SOC in CH were lower than NH when compared under the semi-arid environmental conditions found in southwestern North Dakota. Over the study period, the undisturbed grass control plots had increases in STC and SOC levels in the soil profile of 3.90 kg·m−2 and 3.34 kg·m−2, respectively. Restored grass on the NH area with grazing showed increases in STC and SOC values of 2.11 and 1.26 kg·m−2, respectively, while without grazing, profile STC and SOC had values of 3.80 and 3.28 kg·m−2, respectively. Restored grass on the CH area showed increases in profile STC and SOC values of 0.55 and 1.96 kg·m−2, respectively, for the grazed plots and 0.78 and 2.11 kg·m−2, respectively, when left ungrazed. Soil inorganic C, though present in the soils, did not significantly change during the study. The lower C accumulation in the CH plots may be due to a lag time in the establishment of mycorrhizal associations with the seeded species, the inoculums of which were already present in the NH soils. Changes in STC were likely due to changes in water relationships in the soil profile where management changes affected water infiltration and its movement causing leaching of SIC below the 60 cm depth evaluated. Soils under undisturbed grassland continue to accumulate carbon while soils of the disturbed grassland or cropped prior to re-establishing grass showed losses that occurred due to either accumulating C at a lower rate or perhaps to C loss during the initial establishment period (1–2 years).

Yellajosula, Gayatri↗
DOE OSTI2022

Alphavirus Particles Can Assemble with an Alternate Triangulation Number

Alphaviruses are spherical, enveloped RNA viruses primarily transmitted by mosquitoes, and cause significant arthritogenic and neurotropic disease in humans and livestock. Previous reports have shown that—in contrast to prototypical icosahedral viruses—alphaviruses incorporate frequent defects, and these may serve important functions in the viral life cycle. We confirm the genus-wide pleomorphism in live viral particles and extend our understanding of alphavirus assembly through the discovery of an alternate architecture of Eastern equine encephalitis virus (EEEV) particles. The alternate T = 3 icosahedral architecture differs in triangulation number from the classic T = 4 icosahedral organization that typifies alphaviruses, but the alternate architecture maintains the quasi-equivalence relationship of asymmetric units. The fusion spike glycoproteins are more loosely apposed in the T = 3 form with corresponding changes in the underlying capsid protein lattice. This alternate architecture could potentially be exploited in engineering alphavirus-based particles for delivery of alphaviral or other RNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Deoptimization of FMDV P1 Region Results in Robust Serotype-Independent Viral Attenuation

Foot-and-mouth disease (FMD), caused by the FMD virus (FMDV), is a highly contagious disease of cloven-hoofed livestock that can have severe economic impacts. Control and prevention strategies, including the development of improved vaccines, are urgently needed to effectively control FMD outbreaks in endemic settings. Previously, we employed two distinct strategies (codon pair bias deoptimization (CPD) and codon bias deoptimization (CD)) to deoptimize various regions of the FMDV serotype A subtype A12 genome, which resulted in the development of an attenuated virus in vitro and in vivo, inducing varying levels of humoral responses. In the current study, we examined the versatility of the system by using CPD applied to the P1 capsid coding region of FMDV serotype A subtype, A24, and another serotype, Asia1. Viruses carrying recoded P1 (A24-P1Deopt or Asia1-P1Deopt) exhibited different degrees of attenuation (i.e., delayed viral growth kinetics and replication) in cultured cells. Studies in vivo using a mouse model of FMD demonstrated that inoculation with the A24-P1Deopt and Asia1-P1Deopt strains elicited a strong humoral immune response capable of offering protection against challenge with homologous wildtype (WT) viruses. However, different results were obtained in pigs. While clear attenuation was detected for both the A24-P1Deopt and Asia1-P1Deopt strains, only a limited induction of adaptive immunity and protection against challenge was detected, depending on the inoculated dose and serotype deoptimized. Our work demonstrates that while CPD of the P1 coding region attenuates viral strains of multiple FMDV serotypes/subtypes, a thorough assessment of virulence and induction of adaptive immunity in the natural host is required in each case in order to finely adjust the degree of deoptimization required for attenuation without affecting the induction of protective adaptive immune responses.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

African Swine Fever Virus Protein–Protein Interaction Prediction

The African swine fever virus (ASFV) is an often deadly disease in swine and poses a threat to swine livestock and swine producers. With its complex genome containing more than 150 coding regions, developing effective vaccines for this virus remains a challenge due to a lack of basic knowledge about viral protein function and protein–protein interactions between viral proteins and between viral and host proteins. In this work, we identified ASFV-ASFV protein–protein interactions (PPIs) using artificial intelligence-powered protein structure prediction tools. We benchmarked our PPI identification workflow on the Vaccinia virus, a widely studied nucleocytoplasmic large DNA virus, and found that it could identify gold-standard PPIs that have been validated in vitro in a genome-wide computational screening. We applied this workflow to more than 18,000 pairwise combinations of ASFV proteins and were able to identify seventeen novel PPIs, many of which have corroborating experimental or bioinformatic evidence for their protein–protein interactions, further validating their relevance. Two protein–protein interactions, I267L and I8L, I267L__I8L, and B175L and DP79L, B175L__DP79L, are novel PPIs involving viral proteins known to modulate host immune response.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Endemic Seroprevalence and Farmer Control Measures of Anthrax Among Ruminate Animals in Pakistan

Anthrax, caused by Bacillus anthracis (B. anthracis), is an important zoonotic disease of livestock that poses a threat to public safety. The present study aimed to determine the seroprevalence of Bacillus anthracis in sheep and cattle in endemic areas (Punjab and Balochistan provinces) of Pakistan by enzyme-linked immunosorbent assay (ELISA). Crosssectional survey was also done to assess the control measures of the farmers. Out of 401 serum samples from sheep and cattle, a total of 68 (16.9%) samples were seropositive for anti-PA antibodies; seroprevalence of B. anthracis in sheep and cattle was 22.11% (48/217) and 10.86% (20/184), respectively. Seroprevalence was significantly higher (p<0.05) in Baluchistan province (33.3%, 44/132) compared to Punjab province (8.92%, 24/269). Most farmers (65.90%, 29/44) were not disposing carcasses as recommended. Around 77.28%, 17/22 of the veterinary officials reported the nonavailability of vaccine against anthrax and 63.63% (14/22) stated the lack of cold chain for the vaccine storage and transportation. We concluded that seroprevalence of B. anthracis in unvaccinated sheep and cattle is evidence that the pathogen is circulating in Baluchistan and Punjab provinces. So must applied an active surveillance and, strengthened veterinary practices vaccination programs to control anthrax outbreaks in endemic areas.

59 BASIC BIOLOGICAL SCIENCES↗